PDB-2v8h: Crystal structure of mutant E159A of beta-alanine synthase from S...

ID or keywords:

Entry

Database: PDB / ID: 2v8h

Title

Crystal structure of mutant E159A of beta-alanine synthase from Saccharomyces kluyveri in complex with its substrate N-carbamyl-beta- alanine

Components

BETA-ALANINE SYNTHASE

Keywords

HYDROLASE / AMIDOHYDROLASE / ALPHA AND BETA PROTEIN / DI-ZINC CENTER / COMPLEX WITH N-CARBAMYL-BETA-ALANINE

Function / homology

Function and homology information

beta-ureidopropionase activity / beta-ureidopropionase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines / metal ion binding
Similarity search - Function

Biological species

SACCHAROMYCES KLUYVERI (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Lundgren, S. / Andersen, B. / Piskur, J. / Dobritzsch, D.

Citation

Journal: J.Biol.Chem. / Year: 2007
Title: Crystal Structures of Yeast -Alanine Synthase Complexes Reveal the Mode of Substrate Binding and Large Scale Domain Closure Movements.
Authors: Lundgren, S. / Andersen, B. / Piskur, J. / Dobritzsch, D.

History

Deposition	Aug 8, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 2, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2v8h.cif.gz	359.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2v8h_validation.pdf.gz	484.6 KB	Display	wwPDB validaton report
Full document	2v8h_full_validation.pdf.gz	493.8 KB	Display
Data in XML	2v8h_validation.xml.gz	68.5 KB	Display
Data in CIF	2v8h_validation.cif.gz	98 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v8/2v8h ftp://data.pdbj.org/pub/pdb/validation_reports/v8/2v8h	HTTPS FTP

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Related structure data

Related structure data	2v8dC 2v8gC 2v8vC 1r43S 1r3n C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2v8g-2 2v8g-1 2vl1-2 2vl1-1 1jmj-d 6zpg-d 6i1n-d 4f8y-d 3pfo-d 3lcm-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (5)

Deposited unit

A: BETA-ALANINE SYNTHASE

B: BETA-ALANINE SYNTHASE

C: BETA-ALANINE SYNTHASE

D: BETA-ALANINE SYNTHASE

hetero molecules

209 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: BETA-ALANINE SYNTHASE

B: BETA-ALANINE SYNTHASE

hetero molecules

defined by author&software
105 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: BETA-ALANINE SYNTHASE

D: BETA-ALANINE SYNTHASE

hetero molecules

defined by author&software
105 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	49.780, 218.300, 81.580
Angle α, β, γ (deg.)	90.00, 92.19, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LEU	LEU	TRP	TRP	3	A	A	28 - 52	27 - 51
2	1	LEU	LEU	TRP	TRP	3	B	B	28 - 52	27 - 51
3	1	LEU	LEU	TRP	TRP	3	C	C	28 - 52	27 - 51
4	1	LEU	LEU	TRP	TRP	3	D	D	28 - 52	27 - 51
1	2	HIS	HIS	VAL	VAL	3	A	A	57 - 189	56 - 188
2	2	HIS	HIS	VAL	VAL	3	B	B	57 - 189	56 - 188
3	2	HIS	HIS	VAL	VAL	3	C	C	57 - 189	56 - 188
4	2	HIS	HIS	VAL	VAL	3	D	D	57 - 189	56 - 188
1	3	SER	SER	HIS	HIS	3	A	A	196 - 455	195 - 454
2	3	SER	SER	HIS	HIS	3	B	B	196 - 455	195 - 454
3	3	SER	SER	HIS	HIS	3	C	C	196 - 455	195 - 454
4	3	SER	SER	HIS	HIS	3	D	D	196 - 455	195 - 454
1	4	ZN	ZN	ZN	ZN	4	A	E	500
2	4	ZN	ZN	ZN	ZN	4	B	I	500
3	4	ZN	ZN	ZN	ZN	4	C	M	500
4	4	ZN	ZN	ZN	ZN	4	D	Q	500
1	5	URP	URP	URP	URP	4	A	G	600
2	5	URP	URP	URP	URP	4	B	K	600
3	5	URP	URP	URP	URP	4	C	O	600
4	5	URP	URP	URP	URP	4	D	S	600

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.669, 0.015, 0.743), (-0.011, -1, 0.011), (0.743, -0.001, 0.669)	0.698, -0.43239, -0.36062
2	given	(-0.791, 0.002, -0.611), (0.006, -1, -0.011), (-0.611, -0.012, 0.791)	66.60809, 74.71856, 23.24108

#1: Protein	BETA-ALANINE SYNTHASE Mass: 51948.773 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-455 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES KLUYVERI (fungus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q96W94, beta-ureidopropionase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-URP / N-(AMINOCARBONYL)-BETA-ALANINE / N-CARBAMYL-BETA-ALANINE / BETA-UREIDOPROPIONATE Mass: 132.118 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₈N₂O₃
#4: Chemical	ChemComp-BCN / BICINE Mass: 163.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄ / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 956 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, GLU 159 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 159 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, GLU 159 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 159 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLU 159 TO ALA ENGINEERED RESIDUE IN CHAIN D, GLU 159 TO ALA
Sequence details	THE N-TERMINAL METHIONINE IS ABSENT, MOST LIKELY DUE TO POSTTRANSLATIONAL MODIFICATION THE LAST 20 ...THE N-TERMINAL METHIONINE IS ABSENT, MOST LIKELY DUE TO POSTTRANSLATIONAL MODIFICATION THE LAST 20 AMINO ACIDS CORRESPOND TO THE C-TERMINAL HIS-TAG E159 OF THE DEPOSITED SEQUENCE IS REPLACED BY ALANINE IN THIS MUTANT

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.07 Å³/Da / Density % sol: 40.7 % / Description: NONE
Crystal grow	pH: 8.75 / Details: PEG 6000, TRIS PH 8.5, BICINE PH 9.0, LICL

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
Detector	Type: ADSC CCD / Detector: CCD / Date: Sep 10, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.931 Å / Relative weight: 1
Reflection	Resolution: 2→20 Å / Num. obs: 116114 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / B_iso Wilson estimate: 28.4 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 9.48
Reflection shell	Resolution: 2→2.1 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.27 / Mean I/σ(I) obs: 4.84 / % possible all: 99.3

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R43

1r43

Resolution: 2→19.76 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.938 / SU B: 8.095 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.208	5792	5 %	RANDOM
R_work	0.178	-	-	-
obs	0.18	110321	99.6 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 27.59 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.07 Å²	0 Å²	-0.22 Å²
2-	-	-3.35 Å²	0 Å²
3-	-	-	0.27 Å²

Refinement step

Cycle: LAST / Resolution: 2→19.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13359	0	88	956	14403

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	14010
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.096	1.943	19028
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.472	5	1801
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.352	24.406	665
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.379	15	2298
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.362	15	76
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	2043
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	10872
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.181	0.2	6140
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.297	0.2	9474
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.202	0.2	899
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.154	0.2	80
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.177	0.2	30
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.36	1.5	8979
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.592	2	13948
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.185	3	5823
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.827	4.5	5044
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1632	tight positional	0.04	0.05
2	B	1632	tight positional	0.03	0.05
3	C	1632	tight positional	0.03	0.05
4	D	1632	tight positional	0.04	0.05
1	A	10	medium positional	0.29	0.5
2	B	10	medium positional	0.26	0.5
3	C	10	medium positional	0.27	0.5
4	D	10	medium positional	0.74	0.5
1	A	1440	loose positional	0.19	5
2	B	1440	loose positional	0.19	5
3	C	1440	loose positional	0.2	5
4	D	1440	loose positional	0.22	5
1	A	1632	tight thermal	0.09	0.5
2	B	1632	tight thermal	0.06	0.5
3	C	1632	tight thermal	0.06	0.5
4	D	1632	tight thermal	0.07	0.5
1	A	10	medium thermal	0.56	2
2	B	10	medium thermal	0.98	2
3	C	10	medium thermal	0.55	2
4	D	10	medium thermal	0.89	2
1	A	1440	loose thermal	0.9	10
2	B	1440	loose thermal	0.73	10
3	C	1440	loose thermal	0.77	10
4	D	1440	loose thermal	0.82	10

LS refinement shell

Resolution: 2→2.05 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.233	450
R_work	0.204	7969

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.8588	-0.1935	0.0267	1.2232	-0.1469	1.005	-0.0192	0.0471	0.0631	-0.0424	0.0069	-0.1172	-0.1187	0.073	0.0124	-0.1886	-0.0172	0.0195	-0.0633	-0.0034	-0.1322	7.7998	31.5079	4.6444
2	0.3035	-0.0662	0.1404	4.4691	-0.386	0.2936	0.013	0.0155	-0.065	-0.107	0.0062	0.2395	0.0545	-0.0622	-0.0192	-0.1813	-0.0117	0.0218	-0.0585	-0.0104	-0.1332	-10.3598	4.3815	-5.7268
3	0.7794	-0.0531	-0.0601	2.6758	0.2426	0.727	-0.0084	-0.0915	-0.031	0.3312	0.0419	-0.1254	0.0563	-0.0071	-0.0335	-0.0104	0.01	-0.0179	-0.0308	0.0095	-0.0273	-1.3636	-31.8453	8.9743
4	0.3379	0.6242	0.0064	6.0274	0.2328	0.0101	-0.0263	0.0916	-0.0754	-0.4554	-0.0062	-0.2322	0.126	0.0527	0.0325	-0.1106	0.0092	0.0612	-0.0487	-0.0294	-0.1181	3.322	-4.9622	-11.7583
5	0.8645	0.3438	0.042	3.4587	0.2271	0.9427	-0.0046	0.1487	0.0206	-0.2732	-0.0375	-0.0994	-0.0291	-0.0189	0.0421	-0.037	0.0091	-0.014	-0.0356	0.0052	-0.0528	20.0701	68.8847	31.7092
6	0.2276	-1.1318	0.0806	5.6655	-0.3385	0.1345	-0.1254	-0.06	0.0431	0.7377	0.0186	-0.3124	-0.1909	0.0343	0.1067	0.0242	-0.0131	-0.059	-0.0445	-0.0146	-0.0864	27.308	42.0529	51.8437
7	0.9755	0.1831	0.0842	1.7009	-0.1528	1.0278	0.0142	0.0047	-0.0481	0.0593	-0.0466	-0.0421	0.0992	0.0746	0.0324	-0.1764	0.0177	0.0187	-0.0721	0.0016	-0.1212	31.5624	5.6779	35.1952
8	0.231	-0.4009	0.1418	4.2638	-0.5126	0.5254	-0.0612	-0.0744	-0.0206	0.3534	0.0057	0.4231	-0.1004	-0.1107	0.0555	-0.1175	0.0058	0.0838	-0.0464	-0.0101	-0.06	13.4483	32.2626	47.0738

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	28 - 246
2	X-RAY DIFFRACTION	1	A	365 - 458
3	X-RAY DIFFRACTION	1	A	500 - 601
4	X-RAY DIFFRACTION	2	A	247 - 364
5	X-RAY DIFFRACTION	3	B	28 - 246
6	X-RAY DIFFRACTION	3	B	365 - 458
7	X-RAY DIFFRACTION	3	B	500 - 601
8	X-RAY DIFFRACTION	4	B	247 - 364
9	X-RAY DIFFRACTION	5	C	27 - 246
10	X-RAY DIFFRACTION	5	C	365 - 458
11	X-RAY DIFFRACTION	5	C	500 - 601
12	X-RAY DIFFRACTION	6	C	247 - 364
13	X-RAY DIFFRACTION	7	D	28 - 246
14	X-RAY DIFFRACTION	7	D	365 - 458
15	X-RAY DIFFRACTION	7	D	500 - 601
16	X-RAY DIFFRACTION	8	D	247 - 364

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